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PhD Studentships: Fish Ecology of Mesophotic Coral Reef Ecosystems

Dominic Andradi-Brown

University of Oxford

Supervisor(s): Alex Rogers (Oxford) and Dan Exton (Operation Wallacea)

Mesophotic coral reef ecosystems (MCE) occur in tropical regions extending from 30 m to the limit of the photic zone, c. 150 m. These reefs are often connected to shallow coral reef ecosystems, where it is suggested they provide an important reservoir of recruits for coral and fish populations. Existing reef fish studies are highly depth biased mostly < 30 m, making the importance of mesophotic reefs to overall reef resilience in the face of human disturbances such as overfishing largely unknown, with a lack of evidence for whether fish populations on shallow reefs and adjacent MCEs are connected. This study addresses this important information gap by using advanced diving technologies coupled with a newly developed stereo-video system and molecular ecology techniques to better understand fish communities by examining fish biomass distributions and community structure down depth gradients from shallow reefs to MCEs and by exploring the connectivity of MCE fish populations down depth gradients with shallow reefs and between mesophotic reefs. This project is being conducted in partnership with Operation Wallacea with fieldwork principally based at their field site on Utila, Honduras where MCEs connected to shallow reefs have been identified but are unstudied. The aims of the project are twofold, first to Investigate biomass and community structure. Fisheries value and ecological service provision requires biomass to be quantified as it provides a better indication of functional pressure exerted by a fish-feeding guild than richness or abundance. Fish biomass along transects will be assessed by stereo-video surveys capturing the shallow reef to MCE gradient at various fished and protected sites. Biomass will be standardised using fish length-weight relationships, through data from local fisheries monitoring programmes to obtain local length to weight ratios, but for any fish species not caught locally, through available datasets (e.g. Fishbase). To allow patterns in fish biomass and community structure to be explained, benthic composition will be quantified using point intercept video transects, quantifying coral (genera and morphology), algal and other coverage. Physical parameters will also be recorded including temperature, light and turbidity and HOBO loggers for detailed year-round temperature and light readings. The second aim is to Investigate connectivity in MCE fish populations. Levels of population connectivity between populations of depth-generalist fish species with residents found on both shallow reefs and MCEs are not known. This has major implications for conservation and sustainable management of MCE fisheries, as well as the design and location of marine protected area networks. Many studies have demonstrated the ability of molecular techniques such as microsatellites to identify population structure; these protocols can be applied to assess connectivity down depth gradients and between MCE specialist species on small spatial scales. Non-lethal fin clippings will be collected from fish using a hand net and a clove oil anaesthetic mix. Care will be taken to return individuals to the reef where they were caught. To assess connectivity along depth gradients, samples of depth-generalist reef associated fish will be collected at different depths at several sites. To assess population connectivity between MCEs, an MCE specialist fish species will be identified samples collected at several sites. Contact: Ocean Research and Conservation Group Department of Zoology University of Oxford The Tinbergen Building South Parks Road Oxford OX1 3PS UK Email: Twitter: @dandradibrown URL:

PhD Studentships: Assessing and predicting the impacts of non-native fish parasites: From Hosts to Ecosystems

Josie Pegg

Bournemouth University

Supervisor(s): Robert Britton and Demetra Andreou

The global introduction rate of freshwater fish has doubled in the last thirty years, primarily through fish movements in the aquaculture industry. When fish are moved from their natural range and introduced into a new range, they are likely to be host to a number of parasites. Whilst some of these parasites might be lost during the introduction process, often some will remain. If transmitted to native species, infection consequences can include pathological damage and, potentially, modifications to host behaviour, fitness and energetics. Given that native parasites have recently been shown to play important roles in food webs through, for example, increasing connectivity, nestedness and robustness, then further introductions of parasites into ‘infectious food webs’ have potential to modify these food web properties.

My research explores this using three non-native fish parasites introduced into UK freshwaters in order to identify their consequences for individual hosts, assess how these scale up into population and community effects, and determine their modifications to the structure of the invaded food web. Three non-native parasites will be studied which represent groups with varying complexity in their lifecycles so that they can demonstrate how, for example, the number of hosts in the life cycle affects food web structure.

Ergasilus briani has a simple life cycle, involving host-to-host transmission in their preferred host species of roach Rutilus rutilus and common bream Abramis brama. Bothriocephalus acheilognathi has a complex life cycle involving intermediate hosts before their definitive fish host becomes infected, where the final host here is common carp Cyprinus carpio. Anguillicoides crassus also has a complex life cycle but it involves several paratenic hosts (in which the parasite remains immature) before being transmitted to its preferred definitive host, in UK waters the European eel Anguilla anguilla. Transmission to eels is often through predation of a paratenic host.

Using both field case studies and experimental mesocosms the consequences of these parasites for food web structure will be assessed using two principal methods: food web topology and stable isotope analysis.

My report on my attendance at the Canadian Conference For Fisheries Research 2014 is here.


Faculty of Science and Technology
Bournemouth University
Talbot Campus
PooleBH12 5BB

PhD Studentships: The effects of Different Beta-Glucans on fish microflora: Immunomodulation and disease protection

Sarah Harris

Keele University

Supervisor(s): Dave Hoole, Mark Skidmore and Dieter Steinhagen

There is ever increasing pressure on fish populations to meet the demands placed on them both as a food source and an economic commodity. Aquaculture plays a significant role in reducing the need to rely on wild populations, thus helping species that have been pushed dangerously close to extinction to start recovering and, additionally, lessening the strain on wild cohorts of more stable species. As with any farmed population keeping large numbers together can drastically increase the spread of pathogenic disease which may result in high mortality rates and economic losses.

Since the immune protection induced by vaccination tends to be specific to the target pathogen and there is a movement away from more traditional methods of coping with disease outbreaks, such as antibiotic treatments, there is an increased interest in the concept of improving overall health by increasing general immunity. Immunomodulants act by enhancing the general immune defence which can result in a higher rate of survival during infection. Immunomodulative compounds, such as β-glucans, are already widely used within the farming industry and are known to have a positive impact on fish health although the mechanisms behind their actions are still mostly unknown. Additionally, commercial products undergo several stages of processing before reaching the target organism therefore the physical structure of the final immunomodulative components have yet to be fully elucidated.

One of the simplest, least stressful means of exposing fish to β-glucans is to incorporate the compound into the fish feed. Upon consumption, the β-glucans come into contact with the commensal microflora population within the gut. There is an important symbiotic relationship between a host fish and its commensal bacterial population which, if disturbed, may have both positive and negative effects on gut functions and general health. In addition to having immunomodulatory properties upon the host fish, β-glucans can also be utilised as a food source by certain bacterial species. The aim of my research is therefore to establish how immunomodulants affect both the immune response of the host and the ecology of the microflora of the intestine. Whilst there are many publications related to either the host or the microflora as separate entities, there is very little on bridging the gap between the two within ichthyology. Using the common carp (Cyprinus carpio) as a model host and a range of known β-glucan structures, in vitro studies will determine the effects of β-glucans on individual bacterial species and in vivo trials will establish effects on the resident microflora population and the innate immune responses in the gut of the host fish.

Another mode of exposing fish to β-glucans is to add them as a bathing agent. This has been shown to have positive health benefits including increasing the rate of wound healing in carp, but the effect this has on the environmental microflora has not yet been studied. In order to establish the extent the inclusion of known β-glucan structures are able to alter waterborne microflora populations, molecular microbiological methods will be employed to analyse closed circulation systems both with and without the presence of the selected host fish.

This project is a development of the work undertaken under the auspices of the EU ITN “Nemo” which established the effect of MacroGard®, a commercially available β-1,3/1,6-glucan, on the immune status and health of common carp.


School of Life Sciences
Keele University

LinkedIn: Sarah Harris

PhD Studentships: Reef Structural Complexity and the Dwindling Habitat for Diverse Caribbean Fish Communities

Charlie Dryden

Newcastle University

Supervisor(s): Nick Polunin & Steve Newman

Scleractinian corals are ‘ecosystem engineers’, providing most of the foundations of the coral reef ecosystem, specifically creating a three-dimensional physical habitat and micro-climatic conditions for a plethora of species and ecosystem services. Corals act as a refuge from predators, provide habitat surfaces for prey and offer nesting sites for brooding species. Threats to the existence of coral reefs such as climate-related bleaching, diseases, nutrient susceptibility and fishing-related impacts, have created an urgent need to more fully understand the role corals, and the habitat they create, play in supporting the diverse and abundant coral reef communities.

Early work on coral reef degradation focussed largely on phase shifts from coral to algal dominated states and effects on community structure. This rather ignored the role of the physical structure of the reef sustained by corals. Structural complexity has been correlated with higher levels of diversity in both terrestrial and marine habitats, including coral reefs. However, these findings relied upon simplistic habitat measures and broad community metrics. It is necessary for this relationship to be examined in greater detail to identify which aspects of structural complexity are important to specific components of the community. Related to this, there is scarcely anything known about how mobile species interact with the reef framework. Yet the utilisation of space on reefs by fish is key to predicting how degradation will affect the ecosystem and the humans that rely on them. Such understanding will offer insight into how species, trophic groups and size classes react to loss of habitat structure.

The Caribbean has been undergoing continued losses of structurally complex Acropora spp. and Montastraea spp. of coral since the late 1970s. Stress-tolerant corals that form smaller and less complex colonies, such as Porites spp. and Agaricia spp. have now become relatively more abundant and the consequences of this shift are scarcely known. While the coral cover of Caribbean reefs has been declining for 40 years, changes in fish community structure were negligible until 10 years ago. These changes in the Caribbean fish communities are thus unlikely to be exclusively linked to live coral-cover loss. Unlike their Indo-Pacific counterparts, no Caribbean reef fish are obligately dependent on living corals for food or refuge, therefore decline in reef fish communities appears to more closely relate to generic effects of the loss of reef structure.

Temporal trends in Caribbean reef complexity and community structure have been explored through sparse existing data however, there is at present no methodologically-constrained information on spatial trends in Caribbean regional complexity, yet this is crucial for understanding the current status of reefs, the extent of ongoing changes, and the implications for environmental managers.

This study will examine the concept of structural complexity in natural systems and detail the spatial patterns of reef complexity across 10 Caribbean countries. It will then focus on the relationship between complexity and the fish community and the behavioural interactions between fish and the reef structure.

Marine Science and Technology
Newcastle University NE1 7RU


PhD Studentships: Sensory Ecology, Parasites and Mate Choice in the Guppy, POECILIA RETICULATA

Jessica Stephenson

Cardiff University & Bristol University

Supervisor(s): Joanna Cable & Gabrielle Archard, & Julian Partridge

My research focuses on the way information from different sensory systems (vision and olfaction) interact to inform animal decisions. I am using the guppy-gyrodactylid model system to test how parasitism affects this interaction in a mate choice context. In dissecting the mechanism by which parasitism can alter mate choice in this host, the project will increase understanding of how sexual selection changes in parasitized populations. Furthermore, this could provide an explanation for the maintenance of anomalously high Major Histocompatibility Complex (MHC) allelic diversity in parasitized fish populations.

How an individual’s mate choice preferences change over time is an understudied area of evolutionary ecology. Condition-dependent variation in mate choice preferences between individual female guppies has been demonstrated. It is likely, though little tested, that there is also within-individual variation in preference because condition will change through time. One mechanism by which preferences may vary both between and within individuals is through alteration in the rank females attribute to each of the several cues used during mate choice. These cues in guppies have been well studied; in healthy females mate choice appears to be based largely on visual cues, females prefer males with intense carotenoid colouration and high display rate. The role of olfaction in guppy mate choice has received little attention and is uncertain, though it is through olfaction that animals (including fish) assess MHC compatibility. Susceptibility to parasites is linked to MHC genotype in guppies, so choosing mates based on MHC compatibility is likely to increase guppy reproductive fitness. Olfactory cues may also serve to ‘prime’ the visual system, as has been found in zebrafish. I am using a range of behavioural experiments to test hypotheses relating to condition dependent, within individual variation in the use of information from different sensory modalities in a mate choice context.


Cardiff School of Biosciences,
Biomedical Sciences Building,
Museum Avenue,
CF10 3AX


PhD Studentship: A Genomic approach to the Genetic Impact of an Invasive Congener on a threatened native pond fish

Daniel Jeffries

University of Hull & Cefas-Lowestoft

Supervisor(s): Bernd Hänfling, Lori Lawson-Handley & Gordon Copp

Research on invasive species and invaded communities is essential to understanding and predicting biodiversity change. Furthermore, introduced species are excellent model systems with which to address fundamental questions in biology. However, biological invasions can have dramatic impacts on native species and this appears to be the case for the crucian carp Carassius carassius, which is native to northwestern Europe (including southeast England), and under threat from non-native congeners goldfish C. auratus and gibel (a.k.a. Prussian) carp C. gibelio. Conservation efforts for C. carassius are hampered by the taxonomic ambiguity which exists between C. carassius, C. auratus and C. gibelio; the problems in classifying and identifying separate Carassius spp. have introduced doubt regarding the current distributions of all Carassius spp. Consequently, impact assessment has been difficult; for example, it has only recently been demonstrated that around 70% of pure C. carassius populations in Norfolk, UK have been replaced by non-native Carassius species in the past 30 years.

In order to provide impact assessments in invasive systems, conservation geneticists have previously concentrated their studies on the lowered fitness and adaptability of native species in small populations due to the loss of genetic variability. These studies almost exclusively use near-neutral genetic markers, which cannot be a proxy for genetic variation in genes which have selectively important functions. Furthermore, neutral markers will lose genetic variation more rapidly than those under selection, with there being no correlation between molecular marker heterozygosity and heritabilities. There is likely therefore to be a difference between the impact of bottlenecks and/or climate change on genetic variation in neutral and non-neutral genes. Additionally, the study of hybridisation has been carried out previously using mainly only a small number of molecular markers, which do not have sufficient power to reveal the introgression of single genes. These limitations have left two fundamental evolutionary questions unanswered: to what extent is adaptively important genetic variation affected by bottlenecks in small, isolated populations, and, what are the genetic effects associated with environmental change (through invasive species and climate change) on fragmented populations?

With the development of next-generation sequencing, it is now feasible to address these research gaps. Next generation sequencing techniques allow for genome-wide sequencing, including selectively functional genes, thus providing a better representation of the genetic variation within individuals and populations and allowing for comparison between the behaviour of these genome regions during bottlenecks. Furthermore, these techniques allow for the identification of small regions in the genome of native species that have introgressed from non-natives or vice versa. Simultaneously, the genomic analyses of this system, in conjunction with microsatellite analyses, will shed light on the genetic structure of C. carassius populations in both the UK and continental Europe, providing the means to put forward comprehensive and much needed Biodiversity action plans for this threatened species.


Daniel Jeffries
Evolutionary Biology Group
Hardy Building
University of Hull


PhD Studentship: The Structure and Function of Social Networks in a Marine Predator

David Jacoby

Marine Biological Association & University of Exeter

Supervisor(s): Darren Croft and David Sims

It is well documented that many species of shark exhibit frequent, and often sexually segregated, aggregation behaviour during the resting phase of their diel cycle. This behaviour has been linked in the past to habitat or environmental preferences, foraging opportunities and reproductive behaviour, but little attention has been paid to the role of social preferences in these aggregations. Social network analysis is a theoretical framework which has been recently adapted to explore how animals interact through space and time, and consequently what impact this has on the transmission of information or disease between conspecifics. With elasmobranchs exhibiting a larger brain mass to body mass ratio than teleost fish, there is potential for the formation of complex social systems within these aggregation events but this has never been examined.

This project uses the small spotted catshark (Scyliorhinus canicula) as a model species with which to study social preferences and network construction in elasmobranchs. Using repeatable and controlled laboratory network experiments this project aims to determine the role of kinship and familiarity on the development of social structure in this species and assess how habitat complexity is likely to influence decisions about social behaviour. To give context to the laboratory studies, nearly 50 adult catsharks have been tagged acoustically and are currently being tracked in the wild with passive telemetry receivers on the seabed. Network analysis will not only shed light on the degree of co-occurrence of these sharks in the wild but will also be adapted to understand how environmental variables influence the ways in which individual, or groups of, animals move within and between habitat areas. The technique adapted for this study will have implications for the analysis of telemetry data from a wide variety of both marine and terrestrial animals.


Griffiths, A.M., Jacoby, D.M.P., Casane, D., McHugh, M., Croft, D.P., Genner, M.J. & Sims, D.W. First analysis of multiple paternity in an oviparous shark, the small-spotted catshark (Scyliorhinus canicula L.). Journal of Heredity (in press) doi: 10.1093/jhered/esr112

Jacoby, D.M.P., Croft, D.P. & Sims, D.W. Social behaviour in sharks and rays: analysis, patterns and implications for conservation. Fish and Fisheries (in press) doi: 10.1111/j.1467-2979.2011.00436.x

Jacoby, D.M.P., Busawon, D.S. & Sims, D.W. (2010). Sex and social networking: the role of male presence on social structure of female shark groups. Behavioral Ecology 21, 808-818.


The Marine Biological Association of the UK
The Laboratory
Citadel Hill